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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2022

kynema-fmb [SWR-23-07]

Kynema-FMB (FKA: Kynema) is an open-source performance portable flexible multibody (FMB) dynamics solver designed for time-domain simulations. While originally tailored for wind turbine structural dynamics, the formulation and implementation are those of a general flexible-multidbody dynamics solver that can readily be applied to a wide range of systems. Kynema was designed with a narrow focus, namely to provide a lightweight, fast, accurate FMD solver for coupling to computational-fluid-dynamics (CFD) codes, especially the CFD codes in the Kynema suite, for fluid-structure-interaction (FSI) simulations. Kynema-FMB is equipped to model systems that can be represented as a collection of beams and rigid bodies that are connected through constraints. Degrees of freedom are defined in the inertial/global frame of reference and include displacements and rotations (formally as rotation matrices, but stored as quaternions). The underlying formulation is built on a Lie-group time integrator designed for index-3 differential-algebraic equations, which is second-order accurate in time (Bruls et al., 2012). Beam models are based on geometrically exact beam theory and are discretized as high-order spectral finite elements similar to those in BeamDyn (Wang et al., 2017). The governing equations for a FMD system like a wind turbine constitute a highly nonlinear system of constrained partial-differential equations. Kynema-FMB uses analytical Jacobians in the nonlinear-system solves in each time step. Linear systems use sparse storage and several third-party sparse-linear-system solvers are enabled. Ill conditioning of linear systems is mitigated with preconditioning described in Bottasso et al, 2008. Kynema-FMB is integrated with a simple open-source controller (ROSCO). There is an application programming interface (API) for coupling to geometry-resolved CFD (like that in Sharma et al., 2023) and actuator-force CFD (like that in Kuhn et al., 2025). In the latter, for actuator-line models, Kynema-FMB includes an internal blade-element solver that depends on user-provided lookup tables for coefficients of lift and drag, i.e., aerodynamic polars. Kynema-FMB is written in C++ and leverages Kokkos and Kokkos-Kernels (KokkosEcosystem) as its performance portability layer enabling simulations on both CPU and GPU systems. The repository is equipped with extensive automated testing at the unit and regression/system levels. The following describes the high-level development objectives conceived for Kynema: *Kynema will follow modern software development best practices, including test-driven development (TDD), version control, hierarchical automated testing, and continuous integration (CI) for a robust development environment. *The core data structures are memory efficient and enable vectorization and parallelization at multiple levels. *Data structures are data-oriented to exploit methods for accelerated computing including high utilization of chip resources (e.g., single instruction multiple data (SIMD) instruction sets) and parallelization using GP-GPUs. *The computational algorithms incorporate robust open-source libraries for mathematical operations, resource allocation, and data management. *The API design considers multiple stakeholder needs and ensure integration with existing and future ecosystems for data science, machine learning, and AI. *Kynema-FMB is written in modern C++ and leverages Kokkos as its performance-portability library with inspiration from the kynema stack.

Sprague, MichaelA.↗
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2025

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations (Final Technical Report)

Riparian floodplains are dynamic ecosystems linking terrestrial and riverine systems. These floodplains experience hydrological shifts such as changes in water table height, flooding, and drought and can be ‘hotspots’ of biogeochemical cycling due to shifting sediment moisture (and saturation) and subsurface exchanges of water, nutrients, and other compounds across different sediment layers. Subsurface microbial communities are the primary drivers of biogeochemical processes in floodplains, and thus their structure and function can directly influence both surface and groundwater quality. The microbial nitrogen (N) cycle is particularly important in floodplains as it affects nutrient availability and removal. Two functional guilds of chemoautotrophic (i.e. CO2-fixing) microorganisms are responsible for the first oxidative step of the N cycle, nitrification: ammonia-oxidizing archaea (AOA) and bacteria (AOB) catalyze the oxidation of ammonia to nitrite, while nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate. Despite the critical role nitrification plays in N-cycling in both terrestrial and aquatic ecosystems, our understanding of the diversity, ecophysiology, and activity of nitrifying organisms in subsurface floodplain soils/sediments is extremely limited. To help address this critical knowledge gap, the overarching goal of this project was to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes, with particular emphasis on nitrification, within hydrologically-variable floodplain sediments in the Wind River Basin near Riverton, Wyoming. The three specific objectives of this project were to: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds; (2) determine the guild response to variation in key ecosystem drivers; and (3) develop a dynamic ecosystem model of the microbial N cycle with the Riverton subsurface using community genomic and biogeochemical data collected in the first two objectives. Over the course of this project, we employed both 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrifier communities within 68 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. This project benefitted tremendously from recent advances in high-throughput sequencing technologies coupled with dramatic improvements in the computational tools and algorithms available for analyzing such large, complex genomic datasets. By pairing these cutting-edge genomic approaches with depth-resolved sampling and detailed geochemical analyses of the Riverton floodplain, we have gained novel insights into the structure and function of subsurface nitrifier communities in relation to both hydrology and biogeochemistry. This project resulted in the most detailed and comprehensive characterization of N-cycling floodplain microbial communities to date and will hopefully inspire and pave the way for future studies using similar approaches in other floodplains. Indeed, such information is critical for understanding subsurface biogeochemical cycling and how elemental stores are altered from perturbations initiated by the water cycle within floodplains. Finally, because of the terrestrial-aquatic nature of the Riverton floodplain, results from this project are also of relevance to disciplines such as soil science, estuarine science, limnology & oceanography, biogeochemistry, geobiology, environmental engineering, as well as genomics and data science.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Resolving the Heat of Trimethylaluminum and Water Atomic Layer Deposition Half-Reactions

We report that atomic layer deposition (ALD) is a surface synthesis technique that is characterized by self-limiting reactions between gas-phase precursors and a solid substrate. Although ALD processes have been demonstrated that span the periodic table, a greater understanding of the surface chemistry that affords ALD is necessary to enable greater precision, including area- and site-selective growth. We offer new insight into the thermodynamics and kinetics of the trimethylaluminum (TMA) and H 2 O ALD half-reactions with calibrated and time-resolved in situ pyroelectric calorimetry. The half-reactions produce 3.46 and 2.76 eV/Al heat, respectively, which is greater than the heat predicted by computational models based on crystalline Al 2 O 3 substrates and closely aligned with the heat predicted by standard heats of formation. The pyroelectric thin-film calorimeter offers submilisecond temporal resolution that uniquely and clearly resolves precursor delivery and reaction kinetics. Both half-reactions are observed to exhibit multiple kinetic rates, with average TMA half-reaction rates at least 2 orders of magnitude faster than the H 2 O half-reaction kinetics. Comparing the experimental heat with published computational literature and additional first-principles modeling highlights the need to refine our models and mechanistic understanding of even the most ubiquitous ALD reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Genome-resolved metagenomics and metatranscriptomics of microbial communities in three meander-bound floodplain soils along the East River, Colorado.

This dataset comprises paired environmental and genomic data for soil samples collected across meander-bound floodplains G (ERMG), L (ERML) and Z (ERMZ). A total of 96 soil samples (32 per floodplain) from the ~ 10-25 cm layer were collected in September 2015, during base flow conditions. An additional 32 soil samples were collected from ERML in September 2016, including three samples from a depth just above the water table. A subset of samples (14) collected in 2016 were used for metatranscriptomics as well as metagenomics. The data package includes: 1) A spread sheet with sample names, location and depth by meander-bound floodplain. 2) Total organic carbon (TOC), total inorganic carbon (TIC), total carbon (TC = TOC + TIC), total nitrogen (TN), and the TOC to TN ratio (TOC:N) from 2015 subsamples. 3) Soil chemistry for 2016 subsamples. 4) A spread sheet with elevation, Easting, Northing, and topographic position index (TPI) for each site sampled in 2015. 5) A kml file, which can be viewed in Google Earth, with the locations of the 96 soil sampling sites along the East River Watershed Floodplain in Colorado. Metagenomics and metatranscriptomics data, as well as reconstructed genomes, are available elsewhere (see data package methods and bioRxiv preprint for links to the data). 6) Two sets of reconstructed genomes with overlapping members (see bioRxiv preprint for description and associated data). Metagenomes and metatranscriptomes are available elsewhere (see data package methods and bioRxiv preprint). To view tar.gz files, the following software can be used: https://www.gnu.org/software/tar/, https://www.7-zip.org/.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Real-time elemental analysis of liquids for process monitoring using laser-induced breakdown spectroscopy with a liquid wheel sampling approach

This article presents an engineered sampling system that used a rotating wheel to form a thin liquid layer, permitting the use of laser-induced breakdown spectroscopy (LIBS) for in situ, real-time elemental impurity quantification during liquid processing. The sampling approach was demonstrated on eight elements from across the periodic table (Na, Al, K, Ca, Ti, Sr, Mo, and Yb). Univariate and multivariate calibrations were presented for each element. The average value for percent root mean square errors of cross-validation for the multivariate models was 3.64%, highlighting the method's strong prediction accuracy. Additionally, the limits of detection for each analyte were estimated from their univariate models: Na = 0.0532, Al = 18.5, K = 0.105, Ca = 0.273, Ti = 67.7, Sr = 0.640, Mo = 22.4, and Yb = 22.9 μg mL –1 . Finally, a test in which multivariate models were used to monitor a liquid system for 80 min was performed to investigate the real-time monitoring capabilities of this liquid LIBS sampling approach. Rigorous measurements were performed to effectively predict the absence and concentrations of multiple analytes as they were spiked and diluted. This demonstration showed the feasibility of using LIBS for real-time liquid quantification models with estimated precision ≤ 8.1%. Finally, the limitations of this approach and potential future improvements are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Simulations of radiatively cooled magnetic reconnection driven by pulsed power

Magnetic reconnection is an important process in astrophysical environments, as it reconfigures magnetic field topology and converts magnetic energy into thermal and kinetic energy. In extreme astrophysical systems, such as black hole coronae and pulsar magnetospheres, radiative cooling modifies the energy partition by radiating away internal energy, which can lead to the radiative collapse of the reconnection layer. In this paper, we perform two- and three-dimensional simulations to model the MARZ (Magnetic Reconnection on Z) experiments, which are designed to access cooling rates in the laboratory necessary to investigate reconnection in a previously unexplored radiatively cooled regime. These simulations are performed in GORGON, an Eulerian two-temperature resistive magnetohydrodynamic code, which models the experimental geometry comprising two exploding wire arrays driven by 20 MA of current on the Z machine (Sandia National Laboratories). Radiative losses are implemented using non-local thermodynamic equilibrium tables computed using the atomic code Spk, and we probe the effects of radiation transport by implementing both a local radiation loss model and P 1/3 multi-group radiation transport. The load produces highly collisional, super-Alfvénic (Alfvén Mach number M A ≈ 1.5), supersonic (Sonic Mach number M S ≈ 4–5) strongly driven plasma flows which generate an elongated reconnection layer (Aspect Ratio L/δ≈100 , Lundquist number S L ≈ 400). The reconnection layer undergoes radiative collapse when the radiative losses exceed the rates of ohmic and compressional heating (cooling rate/hydrodynamic transit rate = τ$^{–1}_{cool}$/τ$^{–1}_{H}$ ≈100); this generates a cold strongly compressed current sheet, leading to an accelerated reconnection rate, consistent with theoretical predictions. Lastly, the current sheet is also unstable to the plasmoid instability, but the magnetic islands are extinguished by strong radiative cooling before ejection from the layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Belowground cross-trophic networks impact CH4 and CO2 emissions in degraded alpine peatlands

Belowground organisms forming complex cross-trophic ecological networks are essential for maintaining peatland carbon stability and energy flow. However, how peatland degradation affects the biodiversity and cross-trophic ecological networks of soil communities remains poorly understood. Here, we examined the degradation effects on soil prokaryotes (i.e., bacteria, archaea), fungi and nematodes in alpine peatlands on the eastern Tibetan Plateau, characterized by varying water table depths (indicating degradation levels). We found that peatland degradation, accompanied by significant shifts in soil moisture and pH (P < 0.05), reduced the taxonomic richness and phylogenetic diversity of prokaryotes, fungi, and nematodes, particularly in deeper soil layers (20–50 cm). Crucially, peatland degradation weakened potential cross-trophic interactions within bipartite networks of prokaryotes-nematodes and fungi-nematodes, resulting in less than 6.5 %–28.8 % of unchanged modules. Degradation-induced changes in soil moisture and pH were identified as primary drivers of biodiversity loss and network restructuring. Furthermore, such changes of belowground cross-trophic networks (particularly prokaryote-nematode) were significantly correlated with greenhouse gas emissions, such as decreased CO2 emissions, maintained CH4 emissions (leading to a higher CH4/CO2 ratio in deep layers), and reduced temperature sensitivity (Q10) of soil respiration. These findings underscore the critical need to protect soil biodiversity and cross-trophic networks in peatlands, particularly under the threat of climate change, to preserve peatland carbon stocks and maintain ecosystem stability. Our findings highlight that belowground cross-trophic networks are pivotal to decipher soil carbon dynamics of degraded peatlands and project the fate of peatland carbon stocks under future climate change scenarios.

Cross-trophic networks↗
DOE OSTI2023

Extending Parsimonious Bayesian Inference

Parsimonious Bayesian inference is a theoretical framework for efficient data assimilation that seeks to balance increased consistency between predictions and training data against corresponding increases in model complexity. Within this framework, over-training is understood as optimization that encodes excessive information within model parameters while only achieving small improvements between predictions and training data. This project aims to develop practical methods of limiting excess model information during optimization. One key observation is that practical heuristics for parsimonious learning in high-dimensions must balance expressivity, i.e. the ability of the model to capture diverse predictions with only a few non-zero parameters, against discoverability, i.e. the ability to train the model with gradient-based optimization and drive parameters to low information states. As such, we developed logical activation functions that are able to adaptively approximate arbitrary truth tables that define Boolean logic operations within a probabilistic framework. These functions have demonstrated the ability to learn exclusive disjunction (XOR) and conditioned disjunction (if [condition] then [result_if_true] else [result_if_false]) within a single layer of a neural network. To efficiently exploit these activation functions to drive parsimonious learning required several other advances within the domain of variational inference. The most efficient form of complexity suppression is structured sparsification, driving most model parameters to zero while achieving the structural coherence among nonzeros needed for bandwidth reduction. Such models are not only far more efficient at suppressing information-theoretic complexity, they also reduce the other forms of complexity (computations, communication, storage, and the number of dependencies needed to evaluate predictions). Aiming to support enhanced sparsification, this project examined new approaches to high-dimensional variational inference that allow us to calibrate and control parameter uncertainty during optimization. By identifying which parameters can sustain sparsifying perturbations with little impact on prediction quality, we can develop better pruning strategies by framing them as approximate Bayesian inference. These advances also open paths to mitigate concerns with deploying advanced learning methods in resource-constrained environments, such as running models on power-limited or communication-limited devices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Warming, permafrost thaw and increased nitrogen availability as drivers for plant composition and growth across the Tibetan Plateau

Permafrost-affected ecosystems are subject to warming and thawing, which can increase the availability of subsurface nitrogen (N) with consequences in otherwise N-limited tundra and alpine vegetation. Here, we quantify the extent of warming and permafrost thawing and the corresponding effects on nitrogen availability and plant growth based on a 20-year survey across 14 sites on the Tibetan Plateau. The survey showed that most sites have been subject to warming and thawing and that the upper permafrost zone across all sites was rich in inorganic N, mainly as ammonium. We further explore the efficiency of plants to utilize 15 N-labelled inorganic N over five years following 15 N addition at the permafrost table far below the main root zone. The 15 N experiment showed that deep-rooted plant species were able to utilize the labelled N. A SEM model suggests that changes in vegetation can be explained by both active layer warming and permafrost thawing and the associated changes in inorganic nitrogen availability. Our results highlight a feedback mechanism of climate warming, in which released plant-available N may favour deep-rooted plants. This can explain important changes in plant composition and growth across the sites on the Tibetan Plateau.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

MOSAIC-CONUS: A Multimodal, Multi-Temporally Paired Dataset for Earth Sciences

Earth embeddings—vector representations of geographic locations indexed in space and time—are emerging as a unifying interface for geospatial AI. However, their quality depends not only on model design, but on how multimodal Earth observation (EO) data are spatially indexed, temporally aligned, and cross-modally associated during pretraining. We introduce MOSAIC-CONUS (Multimodal Observations with Spatially Aligned Imagery, Urban Points of Interest, In-Situ Measurements and Text Captions), a large-scale EO dataset over the contiguous United States, organized around 250,000 stratified point indices that serve as stable spatial keys across seven modalities: active radar, passive optical imagery, lidar-derived elevation, land cover, functional context, hydrometeorological measurements, and textual summaries. Unlike existing EO datasets, MOSAIC-CONUS introduces four contributions not jointly addressed in prior work: 1. an open-source, large-scale multimodal EO corpus structured around point-indexed data designed to support Earth embedding learning; 2. explicit radar-optical pairing tables spanning twelve temporal alignment regimes, formalizing cross-sensor alignment as a controllable variable for analyzing how temporal mismatch across modalities influences learned embeddings quality; 3. a benchmark suite spanning cross-modal retrieval, annual nightlights regression, and basin-held-out streamflow prediction, positioning MOSAIC-CONUS as a benchmark-ready resource for multimodal AI systems; and 4. a language-based embedding layer through co-registered textual summaries, enabling Earth embeddings to function as a queryable interface for agentic AI systems. The dataset and pairing protocols are publicly released.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Advanced Infrastructure Integrity Modeling (AIIM) Onshore Pipeline Database

The Advanced Infrastructure Integrity Modeling (AIIM) Onshore Pipeline Database is an interoperable spatial resource containing critical environmental, operational, and reported stressors tied to publicly available oil and gas pipeline locations across the contiguous U.S. and Alaska. This database contains two layers: 1. Pipeline point locations (‘pipeline_points’) – More than 500,000 points (at every kilometer along pipelines, and end points) to which more than 350 stress-related variables have been appended. 2. Merged pipelines (‘merged_pipelines’) – The original, publicly available pipeline data (see table below) merged together into one feature class.

Carbon Transport↗
DOE OSTI2020

AATTENUATION—The Atmospheric Attenuation Model for CSP Tower Plants: A Look-Up Table for Operational Implementation

Attenuation of solar radiation between the receiver and the heliostat field in concentrated solar power (CSP) tower plants can reduce the overall system performance significantly. The attenuation varies strongly with time and the average attenuation at different sites might also vary strongly from each other. If no site specific attenuation data is available, the optimal plant design cannot be determined and rough estimations of the attenuation effect are required leading to high uncertainties of yield analysis calculations. The attenuation is caused mainly by water vapor content and aerosol particles in the lower atmospheric layer above ground. Although several on-site measurement systems have been developed during recent years, attenuation data sets are usually not available to be included during the plant project development. An Atmospheric Attenuation (AATTENUATION) model to derive the atmospheric transmittance between a heliostat and receiver on the basis of common direct normal irradiance (DNI), temperature, relative humidity, and barometric pressure measurements was developed and validated by the authors earlier. The model allows the accurate estimation of attenuation for sites with low attenuation and gives an estimation of the attenuation for less clear sites. However, the site-dependent coefficients of the AATTENUATION model had to be developed individually for each site of interest, which required time-consuming radiative transfer simulations, considering the exact location and altitude, as well as the pre-dominant aerosol type at the location. This strongly limited the application of the model despite its typically available input data. In this manuscript, a look-up table (LUT) is presented which enables the application of the AATTENUATION model at the site of interest without the necessity to perform the according complex radiative transfer calculations for each site individually. This enables the application of the AATTENUATION model for virtually all resource assessments for tower plants and in an operational mode in real time within plant monitoring systems around the world. The LUT also facilitates the generation of solar attenuation maps on the basis of long-term meteorological data sets which can be considered during resource assessment for CSP tower plant projects. The LUTs are provided together with this manuscript as supplementary files. The LUT for the AATTENUATION model was developed for a solar zenith angle (SZA) grid of 1°, an altitude grid of 100 m, 7 different standard aerosol types and the standard AFGL atmospheres for mid-latitudes and the tropics. The LUT was tested against the original version of the AATTENUATION model at 4 sites in Morocco and Spain, and it was found that the additional uncertainty introduced by the application of the LUT is negligible. With the information of latitude, longitude, altitude above mean sea level, DNI, relative humidity (RH), ambient temperature (Tair), and barometric pressure (bp), the attenuation can be now derived easily for each site of interest.

14 SOLAR ENERGY↗
DOE OSTI2020

From particle attachment to space-filling coral skeletons

Reef-building corals and their aragonite (CaCO 3 ) skeletons support entire reef ecosystems, yet their formation mechanism is poorly understood. Here we used synchrotron spectromicroscopy to observe the nanoscale mineralogy of fresh, forming skeletons from six species spanning all reef-forming coral morphologies: Branching, encrusting, massive, and table. In all species, hydrated and anhydrous amorphous calcium carbonate nanoparticles were precursors for skeletal growth, as previously observed in a single species. The amorphous precursors here were observed in tissue, between tissue and skeleton, and at growth fronts of the skeleton, within a low-density nano- or microporous layer varying in thickness from 7 to 20 µm. Brunauer-Emmett-Teller measurements, however, indicated that the mature skeletons at the microscale were space-filling, comparable to single crystals of geologic aragonite. Nanoparticles alone can never fill space completely, thus ion-by-ion filling must be invoked to fill interstitial pores. Such ion-by-ion diffusion and attachment may occur from the supersaturated calcifying fluid known to exist in corals, or from a dense liquid precursor, observed in synthetic systems but never in biogenic ones. Concomitant particle attachment and ion-by-ion filling was previously observed in synthetic calcite rhombohedra, but never in aragonite pseudohexagonal prisms, synthetic or biogenic, as observed here. Models for biomineral growth, isotope incorporation, and coral skeletons’ resilience to ocean warming and acidification must take into account the dual formation mechanism, including particle attachment and ion-by-ion space filling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Retrieval of the sea spray aerosol mode from submicron particle size distributions and supermicron scattering during LASIC

Abstract. Improved quantification of sea spray aerosol concentration and size is important for determining aerosol effects on clouds and the climate, though attempts to accurately capture the size distribution of the sea spray mode remain limited by the availability of supermicron size distributions. In this work, we introduce a new approach to retrieving lognormal mode fit parameters for a sea spray aerosol mode by combining submicron size distributions with supermicron scattering measurements using a Mie inversion. Submicron size distributions were measured by an ultra-high-sensitivity aerosol spectrometer (UHSAS), and supermicron scattering was taken as the difference between <10 µm and <1 µm three-wavelength integrating nephelometer measurements (NEPH). This UHSAS-NEPH method was applied during background marine periods of the Department of Energy Atmospheric Radiation Measurement Layered Atlantic Smoke Interactions with Clouds (LASIC) campaign on Ascension Island (November 2016–May 2017), when the contribution of sea spray aerosol was expected to represent a large fraction of the aerosol mass and total scattering. Lognormal sea spray modal parameters were retrieved from comparisons between nephelometer measurements and a lookup table of Mie theory-simulated scattering coefficients for low-error solutions that minimized the 0.4–1 µm residual in the UHSAS size distribution. We evaluated the UHSAS-NEPH method with a set of clean marine measurements in the North Atlantic that included supermicron size and chemical measurements, showing that measured supermicron size distributions are needed to constrain the sea spray number concentration but that mass concentration was reasonably characterized using supermicron scattering. For LASIC, the UHSAS-NEPH method retrieved sea spray mode properties for approximately 88 % of the background marine times when the scattering variability and total particle concentration were low (<± 5 Mm−1 and <400 cm−3, respectively), with mass mean diameter ranging from 0.6 to 1.9 µm (1.47 ± 0.17 µm), modal width ranging from 1.1 to 3.97 (2.4±0.3), and mass concentration ranging from 0.18 to 23.0 µg m−3 (8.37. ± 4.1 µg m−3). The measured nephelometer scattering at three wavelengths was found to constrain the mode width marginally at the largest particle sizes in the absence of additional size and chemical measurements for defining parameters for the Mie solutions. Comparing UHSAS-NEPH retrievals to those of a fitting algorithm applied only to the submicron UHSAS number size distribution showed that correlations between retrieved mass concentration and the available mass-based sea spray tracers (coarse scattering, wind speed, and chloride) are low when supermicron measurements are not considered. This work demonstrates the added value of supermicron scattering measurements for retrieving reasonable sea spray mass concentrations, providing the best-available observationally constrained estimate of the sea spray mode properties when supermicron size distribution measurements are not available.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Meteoric 10Be Flux Calibration Data for the East River Watershed, Colorado, USA

This data package contains tabular and geospatial data used to quantify and model meteoric beryllium-10 fluxes in the East River watershed, Colorado, USA. The tabular component includes calibration-site data from five glacial moraine sites and includes environmental variables used to evaluate spatial controls on meteoric 10Be delivery, including elevation, mean annual precipitation (MAP), mean snow depth, and mean snow water equivalent (SWE). These site-level data were used to compare observed fluxes with environmental gradients across the watershed and to evaluate the effects of erosion correction on flux estimates. The package also includes supporting slope and curvature values used to assess topographic inputs to the erosion analysis. A second component of the data package contains updated manuscript tables and regression outputs used to summarize the relationships between meteoric 10Be flux and environmental predictors. These tables include meteoric 10Be sample information and AMS results, site-level environmental values, site-level meteoric 10Be inventory and flux values, watershed-averaged predicted fluxes, soil bulk density measurements, fine-fraction values, soil pH measurements, and regression statistics including slope, intercept, coefficient of determination, and p-value. The regression products include both standard linear regressions and regressions in which the intercept is constrained to pass through zero, and they support the analyses presented in the companion manuscript. Together, these tabular files provide the numerical basis for the manuscript tables and the regression-based interpretation of meteoric 10Be flux variability in a snow-dominated mountain watershed. The geospatial component of the package consists of GeoTIFF raster files used to generate the map products presented in Figures 2 and 6 of the companion manuscript. These rasters represent watershed-scale spatial layers for environmental variables and regression-based predictions of meteoric 10Be flux. This dataset contains comma-separated values files (.csv), Microsoft Excel files (.xlsx), GeoTIFF raster files (.tif), and upporting metadata files, including CSV data dictionaries and readme text files (.csv, .txt). The tabular files can be opened with standard spreadsheet software, and the raster files can be viewed and analyzed in GIS software such as ArcGIS Pro or QGIS. Together, these files document the numerical and spatial datasets used to calibrate and predict meteoric 10Be delivery in the East River watershed.

East River↗
DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗